I have a couple of connection profiles with different "USER LIBRARY LIST"s. I opened a work space .SQL tab so that I could run this statement, select * from QSYS2.LIBRARY_LIST_INFO where TYPE in ('CURRENT','USER'). When I run this statement on each connection profiles, I only see the *LIBL of the base connection based on my user profile. If I run this command through the SQL action (CTRL+R), CL:DSPLIBL, the resulting output shows the correct *LIBL according to the current connection setting seen in "USER LIBRARY LIST".
I am going to assume the run of SQL statements is done through a different server job that must activate each time the statement is run where as the CL:DSPLIBL is run in a constantly connected server job.